FUS regulates a subset of snoRNA expression and modulates the level of rRNA modifications

Abstract

FUS is a multifunctional protein involved in many aspects of RNA metabolism, including transcription, splicing, translation, miRNA processing, and replication-dependent histone gene expression. In this work, we show that FUS depletion results in the differential expression of numerous small nucleolar RNAs (snoRNAs) that guide 2’-O methylation (2’-O-Me) and pseudouridylation of specific positions in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Using RiboMeth-seq and HydraPsiSeq for the profiling of 2’-O-Me and pseudouridylation status of rRNA species, we demonstrated considerable hypermodification at several sites in HEK293T and SH-SY5Y cells with FUS knockout (FUS KO) compared to wild-type cells. We observed a similar direction of changes in rRNA modification in differentiated SH-SY5Y cells with the FUS mutation (R495X) related to the severe disease phenotype of amyotrophic lateral sclerosis (ALS). Furthermore, the pattern of modification of some rRNA positions was correlated with the abundance of corresponding guide snoRNAs in FUS KO and FUS R495X cells. Our findings reveal a new role for FUS in modulating the modification pattern of rRNA molecules, that in turn might generate ribosome heterogeneity and constitute a fine-tuning mechanism for translation efficiency/fidelity. Therefore, we suggest that increased levels of 2’-O-Me and pseudouridylation at particular positions in rRNAs from cells with the ALS-linked FUS mutation may represent a possible new translation-related mechanism that underlies disease development and progression.

LncRNA CHKB-DT Downregulation Enhances Dilated Cardiomyopathy Through ALDH2

“…33 FUS is a multifunctional protein involved in almost all aspects of mRNA metabolism including mRNA stability, transcription, splicing, miRNA processing, and translation. 34,35 Indeed, FUS is largely a nuclear protein implicated in transcription and posttranscriptional maturation/processing of pre-mRNAs, it is necessary to investigate the regulation of FUS on ALDH2 transcription. First, we performed chromatin immunoprecipitation-PCR assays using antibodies that recognize FUS or RNAP II to evaluate their binding event on the ALDH2 gene promoter.…”

Maturation of small nucleolar RNAs: from production to function

“…Fused in Sarcoma (FUS) is an RNA/DNA-binding protein present in both the nucleus and cytoplasm with significant roles in binding, splicing and transporting RNAs [ 217 ]. It was recently shown that FUS interacts with snoRNAs and that loss of FUS expression can result in increased snoRNA expression and alter both pseudouridylation and 2’-O-methylation levels in rRNA and spliceosomal small nuclear RNAs [ 218 ]. Crosslinking immunoprecipitation followed by sequencing (CLIP-seq) and RNA immunoprecipitation (RIP) experiments showed that FUS interacts with snoRNAs at sites that overlap the snoRNAs’ host genes.…”

“…However, previous studies suggest that FUS binds introns of genes [ 219 ]. Furthermore, knockout experiments in cell lines suggest that FUS binds snoRNAs prior to snoRNP assembly, as there is no change in core protein expression levels upon knockout of FUS [ 218 ]. Loss of FUS expression leads to defects in splicing, which may be related to the role FUS plays in modulating spliceosomal RNA modification [ 219 ].…”

Imprinted small nucleolar RNAs: Missing link in development and disease?

“…In neuropsychiatric disorders, SNORD114‐26 was downregulated in individuals with major depressive disorder (MDD), and similar expression was noted for SNORD114‐10 in the hippocampus of suicide victims (Glavan et al, 2021; Mahajan et al, 2018). The expression pattern of the snoRNAs from this cluster varies widely in neurodegenerative disorders such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS) (Fitz et al, 2021; Gawade et al, 2023).…”